Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community
2014
Preuzimanje 🢃
Autori
Ćirić, MilicaMoon, Christina D.
Leahy, Sinead C.
Creevey, Christopher J.
Altermann, Eric
Attwood, Graeme T.
Rakonjac, Jasna
Gagić, Dragana
Članak u časopisu (Objavljena verzija)
Metapodaci
Prikaz svih podataka o dokumentuApstrakt
Background: In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical, considering that the metasecretome open reading frames (ORFs) comprise only 10% to 30% of total metagenome, and are poorly represented in the dataset due to overall low coverage of metagenomic gene pool, even in large-scale projects. Results: By combining secretome-selective phage display and next-generation sequencing, we focused the sequence analysis of complex rumen microbial community on the metasecretome component of the metagenome. This approach achieved high enrichment (29 fold) of secreted fibrolytic enzymes from the plant-adherent microbial community of the bovine rumen. In particular, we identified hundreds of heretofore rare modules belonging to cellulosomes,... cell-surface complexes specialised for recognition and degradation of the plant fibre. Conclusions: As a method, metasecretome phage display combined with next-generation sequencing has a power to sample the diversity of low-abundance surface and secreted proteins that would otherwise require exceptionally large metagenomic sequencing projects. As a resource, metasecretome display library backed by the dataset obtained by next-generation sequencing is ready for i) affinity selection by standard phage display methodology and ii) easy purification of displayed proteins as part of the virion for individual functional analysis.
Ključne reči:
Surface and secreted proteins / Rumen / Phage display / Nxt generation sequencing / Metagenomics / CellulosomeIzvor:
BMC Genomics, 2014, 15Izdavač:
- BMC, London
Finansiranje / projekti:
- New Zealand Ministry of Business, Innovation and Employment [C10X0803]
- Institute of Fundamental Sciences (Massey University)
- Biotechnology and Biological Sciences Research Council [BBS/E/W/10964A01C, BBS/E/W/10964A01A, BBS/E/W/10964A01B] Funding Source: researchfish
- BBSRC [BBS/E/W/10964A01A, BBS/E/W/10964A01B, BBS/E/W/10964A01C] Funding Source: UKRI
DOI: 10.1186/1471-2164-15-356
ISSN: 1471-2164
PubMed: 24886150
WoS: 000336673800001
Scopus: 2-s2.0-84901410187
Institucija/grupa
Institut za molekularnu genetiku i genetičko inženjerstvoTY - JOUR AU - Ćirić, Milica AU - Moon, Christina D. AU - Leahy, Sinead C. AU - Creevey, Christopher J. AU - Altermann, Eric AU - Attwood, Graeme T. AU - Rakonjac, Jasna AU - Gagić, Dragana PY - 2014 UR - https://imagine.imgge.bg.ac.rs/handle/123456789/718 AB - Background: In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical, considering that the metasecretome open reading frames (ORFs) comprise only 10% to 30% of total metagenome, and are poorly represented in the dataset due to overall low coverage of metagenomic gene pool, even in large-scale projects. Results: By combining secretome-selective phage display and next-generation sequencing, we focused the sequence analysis of complex rumen microbial community on the metasecretome component of the metagenome. This approach achieved high enrichment (29 fold) of secreted fibrolytic enzymes from the plant-adherent microbial community of the bovine rumen. In particular, we identified hundreds of heretofore rare modules belonging to cellulosomes, cell-surface complexes specialised for recognition and degradation of the plant fibre. Conclusions: As a method, metasecretome phage display combined with next-generation sequencing has a power to sample the diversity of low-abundance surface and secreted proteins that would otherwise require exceptionally large metagenomic sequencing projects. As a resource, metasecretome display library backed by the dataset obtained by next-generation sequencing is ready for i) affinity selection by standard phage display methodology and ii) easy purification of displayed proteins as part of the virion for individual functional analysis. PB - BMC, London T2 - BMC Genomics T1 - Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community VL - 15 DO - 10.1186/1471-2164-15-356 ER -
@article{ author = "Ćirić, Milica and Moon, Christina D. and Leahy, Sinead C. and Creevey, Christopher J. and Altermann, Eric and Attwood, Graeme T. and Rakonjac, Jasna and Gagić, Dragana", year = "2014", abstract = "Background: In silico, secretome proteins can be predicted from completely sequenced genomes using various available algorithms that identify membrane-targeting sequences. For metasecretome (collection of surface, secreted and transmembrane proteins from environmental microbial communities) this approach is impractical, considering that the metasecretome open reading frames (ORFs) comprise only 10% to 30% of total metagenome, and are poorly represented in the dataset due to overall low coverage of metagenomic gene pool, even in large-scale projects. Results: By combining secretome-selective phage display and next-generation sequencing, we focused the sequence analysis of complex rumen microbial community on the metasecretome component of the metagenome. This approach achieved high enrichment (29 fold) of secreted fibrolytic enzymes from the plant-adherent microbial community of the bovine rumen. In particular, we identified hundreds of heretofore rare modules belonging to cellulosomes, cell-surface complexes specialised for recognition and degradation of the plant fibre. Conclusions: As a method, metasecretome phage display combined with next-generation sequencing has a power to sample the diversity of low-abundance surface and secreted proteins that would otherwise require exceptionally large metagenomic sequencing projects. As a resource, metasecretome display library backed by the dataset obtained by next-generation sequencing is ready for i) affinity selection by standard phage display methodology and ii) easy purification of displayed proteins as part of the virion for individual functional analysis.", publisher = "BMC, London", journal = "BMC Genomics", title = "Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community", volume = "15", doi = "10.1186/1471-2164-15-356" }
Ćirić, M., Moon, C. D., Leahy, S. C., Creevey, C. J., Altermann, E., Attwood, G. T., Rakonjac, J.,& Gagić, D.. (2014). Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community. in BMC Genomics BMC, London., 15. https://doi.org/10.1186/1471-2164-15-356
Ćirić M, Moon CD, Leahy SC, Creevey CJ, Altermann E, Attwood GT, Rakonjac J, Gagić D. Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community. in BMC Genomics. 2014;15. doi:10.1186/1471-2164-15-356 .
Ćirić, Milica, Moon, Christina D., Leahy, Sinead C., Creevey, Christopher J., Altermann, Eric, Attwood, Graeme T., Rakonjac, Jasna, Gagić, Dragana, "Metasecretome-selective phage display approach for mining the functional potential of a rumen microbial community" in BMC Genomics, 15 (2014), https://doi.org/10.1186/1471-2164-15-356 . .